A series of statistics derived from comparative gene mapping data has been developed to estimate probabilities of synteny (co-occurrence of loci on the same chromosome) in pairwise species comparisons. Currently, the focus is on the following statistical estimates: (1) the within-species synteny for each species, (2) the probability of synteny of a pair of loci in species A given synteny on a specific chromosome in species B (and vice versa), (3) the probability of synteny of a pair of loci in species A given synteny on any chromosome in species B (and vice versa), and (4) the probability of synteny of a pair of loci in one species given synteny in the other species. The definition of these quantities leads to precisely defined probabilities that may be of use in comparative gene mapping studies. For instance, the fourth quantity has been called the "Syntenic Index" and has been used to measure species divergence at the level of chromosomal evolution. Current data sets allow pairwise comparisons to be made among 12 species of primates (122 loci) and among human and 11 other mammalian (nonprimate) species (334 loci).